Variant 3-186853103-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_004797.4(ADIPOQ):c.45T>G(p.Gly15Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 1,614,010 control chromosomes in the GnomAD database, including 13,827 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.11 ( 1139 hom., cov: 32)

Exomes 𝑓: 0.12 ( 12688 hom. )

Consequence

ADIPOQ
NM_004797.4 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.387

Variant links:

Genes affected

ADIPOQ (HGNC:13633): (adiponectin, C1Q and collagen domain containing) This gene is expressed in adipose tissue exclusively. It encodes a protein with similarity to collagens X and VIII and complement factor C1q. The encoded protein circulates in the plasma and is involved with metabolic and hormonal processes. Mutations in this gene are associated with adiponectin deficiency. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Apr 2010]

ADIPOQ links:

ADIPOQ-AS1 (HGNC:):

ADIPOQ-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP7

Synonymous conserved (PhyloP=-0.387 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADIPOQ	NM_004797.4 linkuse as main transcript	c.45T>G	p.Gly15Gly	synonymous_variant	2/3	ENST00000320741.7	NP_004788.1	Q15848A8K660
ADIPOQ	NM_001177800.2 linkuse as main transcript	c.45T>G	p.Gly15Gly	synonymous_variant	3/4		NP_001171271.1	Q15848A8K660B2R773
ADIPOQ-AS1	NR_046662.2 linkuse as main transcript	n.2355A>C		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ADIPOQ	ENST00000320741.7 linkuse as main transcript	c.45T>G	p.Gly15Gly	synonymous_variant	2/3	1	NM_004797.4	ENSP00000320709.2	Q15848
ADIPOQ	ENST00000444204.2 linkuse as main transcript	c.45T>G	p.Gly15Gly	synonymous_variant	3/4	1		ENSP00000389814.2	Q15848
ADIPOQ-AS1	ENST00000422718.1 linkuse as main transcript	n.2226A>C		non_coding_transcript_exon_variant	3/3	5

Frequencies

GnomAD3 genomes

AF:

0.107

AC:

16297

AN:

152042

Hom.:

1141

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0469

Gnomad AMI

AF:

0.0735

Gnomad AMR

AF:

0.185

Gnomad ASJ

AF:

0.207

Gnomad EAS

AF:

0.294

Gnomad SAS

AF:

0.133

Gnomad FIN

AF:

0.0499

Gnomad MID

AF:

0.269

Gnomad NFE

AF:

0.112

Gnomad OTH

AF:

0.161

GnomAD3 exomes

AF:

0.135

AC:

33830

AN:

251118

Hom.:

2832

AF XY:

0.135

AC XY:

18309

AN XY:

135746

show subpopulations

Gnomad AFR exome

AF:

0.0427

Gnomad AMR exome

AF:

0.187

Gnomad ASJ exome

AF:

0.199

Gnomad EAS exome

AF:

0.301

Gnomad SAS exome

AF:

0.133

Gnomad FIN exome

AF:

0.0511

Gnomad NFE exome

AF:

0.115

Gnomad OTH exome

AF:

0.140

GnomAD4 exome

AF:

0.124

AC:

181897

AN:

1461850

Hom.:

12688

Cov.:

AF XY:

0.125

AC XY:

90730

AN XY:

727226

show subpopulations

Gnomad4 AFR exome

AF:

0.0431

Gnomad4 AMR exome

AF:

0.183

Gnomad4 ASJ exome

AF:

0.206

Gnomad4 EAS exome

AF:

0.297

Gnomad4 SAS exome

AF:

0.128

Gnomad4 FIN exome

AF:

0.0521

Gnomad4 NFE exome

AF:

0.118

Gnomad4 OTH exome

AF:

0.139

GnomAD4 genome

AF:

0.107

AC:

16300

AN:

152160

Hom.:

1139

Cov.:

AF XY:

0.109

AC XY:

8131

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.0469

Gnomad4 AMR

AF:

0.185

Gnomad4 ASJ

AF:

0.207

Gnomad4 EAS

AF:

0.293

Gnomad4 SAS

AF:

0.133

Gnomad4 FIN

AF:

0.0499

Gnomad4 NFE

AF:

0.112

Gnomad4 OTH

AF:

0.162

Alfa

AF:

0.103

Hom.:

533

Bravo

AF:

0.115

Asia WGS

AF:

0.210

AC:

728

AN:

3478

EpiCase

AF:

0.129

EpiControl

AF:

0.136

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

ADIPOQ-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 30, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

3.1

DANN

Benign

0.50

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over